Badstuber was injured in their 2-0 league win over VfB Stuttgart and his injury was initially seen as not serious.
Further tests on Sunday, however, revealed the real extent of his injury as Bayern prepare for Wednesday's Champions League game against Manchester City.
Bayern said on Sunday he had sustained a torn thigh muscle tendon and would undergo surgery, ruling him out for a "longer period of time."
"Obviously I am very disappointed at the moment," Badstuber, who had hoped to win back his Germany starting spot soon after coming back this season, said in a statement.
"But I have learned meanwhile how to deal with these situations. I will not give up and do not worry I will come back and pick up where I left off after my long injury break," said the 25-year-old.
(Reporting by Karolos Grohmann, editing by Alan Baldwin)
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